I dealt with this for about a month (1200 miles from home lol) but anyways the 06 manual tranny TJs had a recall on the clutch pedal position switch which you should bypass by reaching under the dash by the pedals disconnect the wiring and use a 20 amp mini fuse on the female side of the connector. This should allow you to start the tj without pushing the clutch if it's out of gear. I would then check the ignition pin actuator inside the steering column it's cheap pot metal so it's brittle and prone to snapping off so pop open the steering column and check or replace that it's not hard to do either if you want some help I'm in Van Buren and unemployed so I have time lol